set_exprs: Assignment method for the new elements of an SCESet object.

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

The assayData slot of an SCESet object holds the expression data matrices. This functions makes it convenient to add new transformations of the expression data to the assayData slot.

Usage

set_exprs(object, name) <- value

## S4 replacement method for signature 'SCESet,ANY,matrix'
set_exprs(object,name)<-value

## S4 replacement method for signature 'SCESet,ANY,'NULL''
set_exprs(object, name) <- value

Arguments

object	a SCESet object.
name	character string giving the name of the slot to which the data matrix is to be assigned (can already exist or not).
value	a numeric or integer matrix matching the dimensions of the other elements of the assayData slot of the SCESet object.

Value

NULL, but adds expression data to the SCESet object

Author(s)

Davis McCarthy

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData = sc_example_counts)
set_exprs(example_sceset, "scaled_counts") <- t(t(counts(example_sceset)) /
colSums(counts(example_sceset)))
get_exprs(example_sceset, "scaled_counts")[1:6, 1:6]

## get rid of scaled counts
set_exprs(example_sceset, "scaled_counts") <- NULL

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.